NGS Read Coverage Calculator

What is read coverage?

Read coverage (also called sequencing depth) is the average number of reads that overlap each base in your reference. A 30× whole-genome sequencing project means every base in the human genome is covered, on average, by 30 reads.

Coverage is the single most important budget knob in an NGS experiment: it sets sensitivity for variant calling, the noise floor for differential expression, and the floor for detecting low-frequency clones in tumor or microbial samples. Picking the right coverage — and the right number of samples — for your platform of choice is what this calculator is for.

The Lander–Waterman relation

For random shotgun sequencing, the expected coverage is:

where C is the average coverage depth, L is the effective read length per read or read pair, N is the number of reads (or read pairs), and G is the genome or target size in base pairs.

The relation reverses cleanly: N = C · G / L gives the reads required to hit a coverage target. Multiply by sample count and you have your project budget. Divide by reads-per-run and you have the number of runs.

Lander & Waterman (1988) derived this in the context of physical mapping; the formula carries over directly to sequencing because both processes are random sampling on a target.

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